Solvent and conformation dependence of amide I vibrations in peptides and proteins containing proline

We present a mixed quantum-classical model for studying the amide I vibrational dynamics (predominantly CO stretching) in peptides and proteins containing proline. There are existing models developed for determining frequencies of and couplings between the secondary amide units. However, these are not applicable to proline because this amino acid has a tertiary amide unit. Therefore, a new parametrization is required for infrared-spectroscopic studies of proteins that contain proline, such as collagen, the most abundant protein in humans and animals. Here, we construct the electrostatic and dihedral maps accounting for solvent and conformation effects on frequency and coupling for the proline unit. We examine the quality and the applicability of these maps by carrying out spectral simulations of a number of peptides with proline in D(2)O and compare with experimental observations.     

Conformational dependence of anharmonic vibrations in peptides: amide-I modes in model dipeptide

The conformational dependence of a set of anharmonic vibrational parameters for the amide-I modes in peptides has been examined at the level of Hartree-Fock theory. By using glycine dipeptide as a model molecule, the phi-psi maps of diagonal and off-diagonal anharmonicities, local mode mixing angle, zero-order local mode frequencies, as well as intermode coupling, were calculated, and all were found to exhibit certain conformational sensitivities. The characteristics of the phi-psi maps of the diagonal and off-diagonal anharmonicities were found to be complementary to each other, and the latter was found to correlate well with that of the mixing angle, reflecting the fact that these anharmonic parameters are interconnected and all determined by the same set of underlying anharmonic force field. The mean values of the diagonal and off-diagonal anharmonicities were found to be 15.7 cm(-1) and 9.9 cm(-1) respectively. The mean value for the two local mode frequency differences was estimated to be 9.7 cm(-1), showing a nondegenerate local mode picture. For significant peptide conformations, the calculated anharmonic parameters were found to be in reasonable agreement with values obtained at the level of density functional theory as well as values obtained with recent two-dimensional infrared experiments.     

On the temperature dependence of amide I frequencies of peptides in solution

The temperature dependence of the amide I vibrational frequencies of peptides in solution was investigated. In D2O, the amide I' bands of both an alpha-helical oligopeptide, the random-coil poly(L-lysine), and the simplest amide, N-methyl acetamide (NMA), exhibit linear frequency shifts of approximately 0.07 cm(-1)/degrees C with increasing temperature. Similar amide I frequency shifts are also observed for NMA in both polar (acetonitrile and DMSO) and nonpolar (1,4-dioxane) organic solvents, thus ruling out hydrogen-bonding strength as the cause of these effects. The experimental NMA amide I frequencies in the organic solvents can be accurately described by a simple theory based on the Onsager reaction field with temperature-dependent solvent dielectric properties and a solute molecular cavity. DFT-level calculations (BPW91/cc-pVDZ) for NMA with an Onsager reaction field confirm the significant contribution of the molecular cavity to the predicted amide I frequencies. Comparison of the computations to experimental data shows that the frequency-dependent response of the reaction field, taken into account by the index of refraction, is crucial for describing the amide I frequencies in polar solvents. The poor predictions of the model for the NMA amide I band in D2O might be due, in part, to the unknown temperature dependence of the refractive index of D2O in the mid-IR range, which was approximated by the available values in the visible region.     

Impact of azaproline on amide cis-trans isomerism: conformational analyses and NMR studies of model peptides including TRH analogues

The beta-turn is a well-studied motif in both proteins and peptides. Four residues, making almost a complete 180 degree-turn in the direction of the peptide chain, define the beta-turn. Several types of the beta-turn are defined according to Phi and Psi torsional angles of the backbone for residues i + 1 and i + 2. One special type of beta-turn, the type VI-turn, usually contains a proline with a cis-amide bond at residue i + 2. In an aza-amino acid, the alpha-carbon of the amino acid is changed to nitrogen. Peptides containing azaproline (azPro) have been shown to prefer the type VI beta-turn both in crystals and in organic solvents by NMR studies. MC/MD simulations using the GB/SA solvation model for water explored the conformational preferences of azPro-containing peptides in aqueous systems. An increase in the conformational preference for the cis-amide conformer of azPro was clearly seen, but the increased stability was relatively minor with respect to the trans-conformer as compared to previous suggestions. To test the validity of the calculations in view of the experimental data from crystal structures and NMR in organic solvents, [azPro(3)]-TRH and [Phe(2), azPro(3)]-TRH were synthesized, and their conformational preferences were determined by NMR in polar solvents as well as the impact of the azPro substitution on their biological activities.     

Single-conformation infrared spectra of model peptides in the amide I and amide II regions: Experiment-based determination of local mode frequencies and inter-mode coupling

Single-conformation infrared spectra in the amide I and amide II regions have been recorded for a total of 34 conformations of three α-peptides, three β-peptides, four α∕β-peptides, and one γ-peptide using resonant ion-dip infrared spectroscopy of the jet-cooled, isolated molecules. Assignments based on the amide NH stretch region were in hand, with the amide I∕II data providing additional evidence in favor of the assignments. A set of 21 conformations that represent the full range of H-bonded structures were chosen to characterize the conformational dependence of the vibrational frequencies and infrared intensities of the local amide I and amide II modes and their amide I∕I and amide II∕II coupling constants. Scaled, harmonic calculations at the DFT M05-2X∕6-31+G(d) level of theory accurately reproduce the experimental frequencies and infrared intensities in both the amide I and amide II regions. In the amide I region, Hessian reconstruction was used to extract local mode frequencies and amide I∕I coupling constants for each conformation. These local amide I frequencies are in excellent agreement with those predicted by DFT calculations on the corresponding (13)C = (18)O isotopologues. In the amide II region, potential energy distribution analysis was combined with the Hessian reconstruction scheme to extract local amide II frequencies and amide II∕II coupling constants. The agreement between these local amide II frequencies and those obtained from DFT calculations on the N-D isotopologues is slightly worse than for the corresponding comparison in the amide I region. The local mode frequencies in both regions are dictated by a combination of the direct H-bonding environment and indirect, "backside" H-bonds to the same amide group. More importantly, the sign and magnitude of the inter-amide coupling constants in both the amide I and amide II regions is shown to be characteristic of the size of the H-bonded ring linking the two amide groups. These amide I∕I and amide II∕II coupling constants remain similar in size for α-, β-, and γ-peptides despite the increasing number of C-C bonds separating the amide groups. These findings provide a simple, unifying picture for future attempts to base the calculation of both nearest-neighbor and next-nearest-neighbor coupling constants on a joint footing.     

Visualization and characterization of the infrared active amide I vibrations of proteins

To facilitate the analysis of frequency-structure correlations in the amide I vibrational spectroscopy of proteins, we investigate visualization methods and spatial correlation functions that describe delocalized vibrations of proteins and protein secondary structures. To study those vibrational modes revealed in infrared spectroscopy, we characterize frequency-dependent bright states obtained from doorway mode analysis. Our visualization methods pictorially color code amplitude and phase of each oscillator within the structure to reveal spatially varying patterns characteristic of excitations within sheets and helices. Spatial correlation functions in the amplitude and phase of amide I oscillators quantitatively address the extent of delocalization and the alpha helical and beta sheet character of these modes. Specifically, we investigate the vibrations of idealized antiparallel beta sheets and alpha helices and perform case studies on three proteins: concanavalin A, myoglobin, and ubiquitin.     

Vibrational-exciton couplings for the amide I, II, III, and A modes of peptides

The couplings between all amide fundamentals and their overtones and combination vibrational states are calculated. Combined with the level energies reported previously (Hayashi, T.; Zhuang, W.; Mukamel, S. J. Phys. Chem. A 2005, 109, 9747), we obtain a complete effective vibrational Hamiltonian for the entire amide system. Couplings between neighboring peptide units are obtained using the anharmonic vibrational Hamiltonian of glycine dipeptide (GLDP) at the BPW91/6-31G(d,p) level. Electrostatic couplings between non-neighboring units are calculated by the fourth rank transition multipole coupling (TMC) expansion, including 1/R3 (dipole-dipole), 1/R4 (quadrupole-dipole), and 1/R5 (quadrupole-quadrupole and octapole-dipole) interactions. Exciton delocalization length and its variation with frequency in the various amide bands are calculated. The simulated infrared amide I and II absorptions and CD spectra of 24 residue alpha-helical motifs (SPE3) are in good agreement with experiment.     

Solvent dependence of PII conformation in model alanine peptides

Alanine residues in two model peptides, the pentapeptide AcGGAGGNH(2) and the 11mer AcO(2)A(7)O(2)NH(2), have been reported to have substantial PII conformation in water. The PII structure in both peptides is sensitive to solvent. In the presence of the organic solvent TFE, the conformation of the pentamer changes from PII to internally H-bonded gamma or beta turns, while the chain with seven alanines forms alpha helix. The PII structure in the 11mer is more stable than that in the shorter peptide as the TFE concentration increases. For the pentamer, a comparison of short-chain aliphatic alcohols to water shows that the PII content decreases in the order water > methanol > ethanol > 2-propanol, linearly according to empirical scales of solvent polarity. Thus, depending on the extent of local solvation as folding progresses, the peptide backbone as modeled by alanine oligomers shifts from PII to internally H-bonded (gamma or beta turn) conformations and to alpha helix in longer segments. On the other hand, the PII content of AcO(2)A(7)O(2)NH(2) increases significantly in the presence of guanidine, as does that of oligoproline peptides, while detergent sodium dodecyl sulfate (SDS) favors alpha helix in this peptide. The shorter peptide does not show a parallel increase in PII with guanidine.     

The dynamics of conformational isomerization in flexible biomolecules. I. Hole-filling spectroscopy of N-acetyl tryptophan methyl amide and N-acetyl tryptophan amide

The conformational isomerization dynamics of N-acetyl tryptophan methyl amide (NATMA) and N-acetyl tryptophan amide (NATA) have been studied using the methods of IR-UV hole-filling spectroscopy (HFS) and IR-induced population transfer spectroscopy (IR-PTS), which were developed for this purpose. Single conformations of these molecules were selectively excited in well-defined NH stretch fundamentals. This excess energy was used to drive conformational isomerization. By carrying out the infrared excitation early in a supersonic expansion, the excited molecules were recooled into their zero-point levels, partially refilling the hole created in the ground state population of one of the conformers, and creating gains in population in other conformers. These changes in population were detected using laser-induced fluorescence downstream in the expansion. In HFS, the IR wavelength is fixed and the UV laser tuned in order to determine where the population went following selective infrared excitation. In IR-PTS, the UV is fixed to monitor the population of a given conformation, and the IR is tuned to record the IR-induced changes in the population of the monitored conformer. Besides demonstrating the capability of the experiment to change the downstream conformational population distribution, the IR-PTS scans were used to extract two quantitative results: (i) The fractional populations of the conformers in the absence of the infrared, and (ii) the isomerization quantum yields for each of the six unique amide NH stretch fundamentals (three conformers each with two amide groups). The method for obtaining quantum yields is described in detail. In both NATMA and NATA, the quantum yields show modest conformational specificity, but only a hint of vibrational mode specificity. The prospects for the hole-filling technique for providing insight into energy flow in large molecules are discussed, leaving a more detailed theoretical modeling to the adjoining paper [Evans et al. J. Chem. Phys. 120, 148 (2004)].     

Single-molecule vibrations, conformational changes, and electronic conductivity of five-membered heterocycles

Using an ultrahigh vacuum scanning tunneling microscope (STM), we have explored the interactions of isolated five-membered heterocycles, pyrrole, thiophene, pyrrolidine, and tetrahydrothiophene, with the Cu(001) surface at 9 K. Pyrrolidine was also studied on the Ag(001) surface. Important distinctions in bonding, vibrational spectra, and vibrationally mediated negative differential resistance were observed with the aid of single-molecule inelastic electron tunneling spectroscopy (STM-IETS).     

Atom-atom interaction model and internal vibrational exciton splittings in organic charge-transfer complexes: Factor group splittings of naphthalene vibrations in several crystalline complexes

Factor group splittings of naphthalene vibrations are experimentally investigated for naphthalene: 2SbCl₃ (C₁₀H₈ - 2SbCl₃), naphthalene: octafluoronaphthalene (C₁₀H₈ : C₁₀F₈), naphthalene: TCNB, and naphthalene: TNB crystalline complexes by Raman spectroscopy and using the isotopically mixed crystal technique. It is found that only 386 cm^?1 mode of C₁₀H₈ shows factor group splittings in the first two complexes. The splitting increases from 5 cm^?1 in pure C₁₀H₈ crystal to 5.5cm^?1 in C₁₀H₈ : 2SbCl₃ but decreases to 1cm^?1 in the C₁₀H₈ : C₁₀F₈ complex. Also as SbCl₃ is successively replaced by SbBr₃ in the complex C₁₀H₈ : 2SbCl₃, the factor group splitting of 386 cm^?1 C₁₀H₈ mode decreases and the mean of the factor group frequencies goes through a minimum near 0.5 mole fraction of SbBr₃. A theoretical calculation using atom-atom potential model and considering only naphthalene-naphthalene interactions predicts that the factor group splitting on 386 cm^?1 band should increase from pure C₁₀H₈ crystal to the C₁₀H₈ :2SbCl₃ crystalline complex and decrease in C₁₀H₈ : C₁₀F₈. However, the calculation also predicts a similar trend for 943 cm^?1 band of naphthalene which shows a factor group splitting of 5 cm^?1 in pure C₁₀H₈ but none in the C₁₀H₈ : 2SbCl₃ complex. Furthermore, the atom-atom interaction model does not explain the effect of SbBr₃ substitution on the factor group splitting. The importance of electrostatic multipole interactions in explaining the behavior of factor group splitting is discussed.     

Ab initio study of catalyzed and uncatalyzed amide bond formation as a model for peptide bond formation: Ammonia-Glycine reactions

As a model reaction for peptide and bond formation, the S_N2 reactions between glycine and ammonia have been studied with and without amine catalysis: using ab initio molecular-orbital methods. For each of the catalyzed and uncatalyzed reactions, two reaction mechanisms have been examined: a two-step and a concerted mechanism. The stationary points of each reaction, including intermediate and transition states, have been identified and free energies calculated for all geometry-optimized reaction species to determine the thermodynamics and kinetics of the reaction. The calculations demonstrate that a second ammonia molecule catalyzes amide bond formation, and that the two-step mechanism is more favorable than the concerted one for the catalyzed reaction, while for the uncatalyzed reaction both mechanisms are competitive.     

Vibrational relaxation pathways of amide I and amide II modes in N-methylacetamide

We studied the vibrational energy relaxation mechanisms of the amide I and amide II modes of N-methylacetamide (NMA) monomers dissolved in bromoform using polarization-resolved femtosecond two-color vibrational spectroscopy. The results show that the excited amide I vibration transfers its excitation energy to the amide II vibration with a time constant of 8.3 ± 1 ps. In addition to this energy exchange process, we observe that the excited amide I and amide II vibrations both relax to a final thermal state. For the amide I mode this latter process dominates the vibrational relaxation of this mode. We find that the vibrational relaxation of the amide I mode depends on frequency which can be well explained from the presence of two subbands with different vibrational lifetimes (~1.1 ps on the low frequency side and ~2.7 ps on the high frequency side) in the amide I absorption spectrum.     

Ab initio modeling of amide I coupling in antiparallel beta-sheets and the effect of 13C isotopic labeling on infrared spectra

Isotopic substitution with 13C on the amide C=O has become an important means of determining localized structural information about peptide conformations with vibrational spectroscopy. Various approaches to the modeling of the interactions between labeled amide sites, specifically for antiparallel two-stranded, beta-forming peptides, were investigated, including different force fields [dipole-dipole interaction vs density functional theory (DFT) treatments], basis sets, and sizes of model peptides used for ab initio calculations, as well as employing models of solvation. For these beta-sheet systems the effect of the relative positions of the 13C isotopic labels in each strand on their infrared spectra was investigated. The results suggest that the interaction between labeled amide groups in different strands can be used as an indicator of local beta-structure formation, because coupling between close-lying C=O groups on opposing chains leads to the largest frequency shifts, yet some alternate placements can lead to intensity enhancements. The basic character of the coupling interaction between labeled modes on opposing strands is independent of changes in peptide length, water solvent environment, twisting of the sheet structure, and basis set used in the calculations, although the absolute frequencies and detailed coupling magnitudes change under each of these perturbations. In particular, two strands of three amides each contain the basic interactions needed to simulate larger sheets, with the only exception that the C=O groups forming H-bonded rings at the termini can yield different coupling values than central ones of the same structure. Spectral frequencies and intensities were modeled ab initio by DFT primarily at the BPW91/6-31G** level for pairs of three, four, and six amide strands. Comparison to predictions of a classical coupled oscillator model show qualitative but not quantitative agreement with these DFT results.     

Hydrolysis of amide bond in histidine-containing peptides promoted by chelated amino acid palladium(II) complexes: dependence of hydrolytic pathway on the coordination modes of the peptides

Hydrolytic reactions between cis-[Pd( -Ala-N,O)Cl₂]⁻ and cis-[Pd( -Ala-N,O)(H₂O)₂]⁺, in which -Ala is alanine coordinated through N and O atoms, and N-acetylated peptides -histidylglycine (MeCO-His-Gly), glycyl- -histidine (MeCO-Gly-His), glycylglycyl- -histidine (MeCO-Gly-Gly-His) and glycyl- -histidylglycine (MeCO-Gly-His-Gly) were studied by ¹H NMR spectroscopy. All reactions were carried out in the pH range 2.0–2.5 and two different temperatures, 22 and 60°C. In the reactions of these two palladium(II) complexes with MeCO-His-Gly, complete hydrolysis of the amide bond involving carboxylic group of histidine occurs in less than 24 h. The cleavage is regioselective. With peptides containing free a carboxylic group of histidine, MeCO-Gly-His and MeCO-Gly-Gly-His, palladium(II) complex promote the cleavage of the MeCO–Gly and Gly–Gly amide bonds. No cleavage of the Gly–His amide bond was observed. The mechanism of these hydrolytic reactions involves release of -Ala ligand and aquation of the palladium(II) complex chelated to the substrate through the imidazole N-3 atom and deprotonated nitrogen atom of the amide bond involving amino group of histidine. This aqua complex represents a catalytically active form different from the initially added catalytically inactive complex. In the reactions of palladium(II) complexes with tripeptide MeCO-Gly-His-Gly, two amide bonds, MeCO–Gly and His–Gly, were cleaved. The mechanism of the cleavage of these amide bonds is correlated with two different palladium(II)–substrate catalytically active forms. These findings contribute to the better understanding of selective cleavage of peptides and proteins and must be taken into consideration in designing new reagents for this purpose.     

Infrared study of the effect of hydration on the amide I band and aggregation properties of helical peptides

The amide I' band of a polypeptide is sensitive not only to its secondary structure content but also to its environment. In this study we show how degrees of hydration affect the underlying spectral features of the amide I' band of two alanine-based helical peptides. This is achieved by solubilizing these peptides in the water pool of sodium bis(2-ethylhexyl)sulfosuccinate reverse micelles with different water contents or w0 values. In agreement with several earlier studies, our results show that the amide I' band arising from a group of dehydrated helical amides is centered at approximately 1650 cm-1, whereas hydration shifts this frequency toward lower wavenumbers. More importantly, temperature-dependent infrared studies further show that these helical peptides undergo a thermally induced conformational transition in reverse micelles of low w0 values (e.g., w0=6), resulting in soluble peptide aggregates rich in antiparallel beta-sheets. Interestingly, however, increasing w0 or water content leads to an increase in the onset temperature at which such beta-aggregates begin to form. Therefore, these results provide strong evidence suggesting that dehydration facilitates aggregate formation and that removal of water imposes a free energy barrier to peptide association and aggregation, a feature that has been suggested in recent simulation studies focusing on the mechanism of beta-amyloid formation.     

Ab initio calculation of anisotropic magnetic properties of complexes. I. Unique definition of pseudospin Hamiltonians and their derivation

A methodology for the rigorous nonperturbative derivation of magnetic pseudospin Hamiltonians of mononuclear complexes and fragments based on ab initio calculations of their electronic structure is described. It is supposed that the spin-orbit coupling and other relativistic effects are already taken fully into account at the stage of quantum chemistry calculations of complexes. The methodology is based on the establishment of the correspondence between the ab initio wave functions of the chosen manifold of multielectronic states and the pseudospin eigenfunctions, which allows to define the pseudospin Hamiltonians in the unique way. Working expressions are derived for the pseudospin Zeeman and zero-field splitting Hamiltonian corresponding to arbitrary pseudospins. The proposed calculation methodology, already implemented in the SINGLE_ANISO module of the MOLCAS-7.6 quantum chemistry package, is applied for a first-principles evaluation of pseudospin Hamiltonians of several complexes exhibiting weak, moderate, and very strong spin-orbit coupling effects.     

Ab initio- and density-functional studies of conformational behaviour of N-formylmethionine in gaseous phase

The current work is a study of the conformational space of the non-ionic N-formylmethionine molecule around its seven structurally significant internal backbone torsional angles at B3LYP/6-31++G(d,p) levels of theory in the gaseous phase. The potential energy surface exploration reveals that a total of 432 different conformers would result if all the possible combinations of the internal rotations were to be considered. A set of twelve conformers of the N-formylmethionine molecule are then further analysed in terms of their relative stabilities, theoretically predicted harmonic vibrational frequencies, HOMO-LUMO energy gaps, ESP charges, rotational constants and dipole moments calculated using MP2/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels. The calculated relative energy-range of the conformers at the MP2 level is 11.08 kcal mol^?1 (1 kcal = 4.1868 kJ), whereas the same obtained at the B3LYP level is 10.02 kcal mol^?1. The results of this study provide a good account of the role of four types of intramolecular H-bonds, namely O…H—O, O…H—N, O…H—C and N…H—C, in influencing the energies of the conformers as well as their conformational and vibrational spectroscopic aspects. The relative stability order of the conformers appears to depend on the level of theory used while the vibrational frequencies calculated at the B3LYP level are in better agreement with the experimental values.